From b7e686996a8c7d28bfe2abb2c2a311a8c4c150d1 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 23 May 2023 17:28:15 -0700 Subject: [PATCH 1/6] update wheel --- .github/workflows/pypi-publish.yaml | 4 ++-- biolink-model.yaml | 5 ++--- setup.cfg | 2 +- setup.py | 2 +- 4 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/workflows/pypi-publish.yaml b/.github/workflows/pypi-publish.yaml index 278cc580bf..5bc42ce803 100644 --- a/.github/workflows/pypi-publish.yaml +++ b/.github/workflows/pypi-publish.yaml @@ -1,8 +1,8 @@ name: Publish Python Package on: - release: - types: [created] + push: + branches: [no_branch_here] jobs: build-n-publish: diff --git a/biolink-model.yaml b/biolink-model.yaml index 7a103ac6e4..985cf58802 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -6,7 +6,7 @@ license: https://creativecommons.org/publicdomain/zero/1.0/ # Version should be kept in sync with primary Git repository release tag -version: 3.4.0 +version: 3.4.1 ## ------------ @@ -527,7 +527,6 @@ slots: in_subset: - translator_minimal - publication type: slot_uri: dct:type description: >- @@ -611,7 +610,7 @@ slots: in_subset: - translator_minimal narrow_mappings: - # there is an interesting debate here: are these terms "narrower" a.k.a. more specialized instances of + # there is an interesting debate here: are these terms "narrower" a.k.a. more specnaialized instances of # 'biolink:synonym' or should they be binned into their respective namesake class of mappings? # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc. - skos:altLabel diff --git a/setup.cfg b/setup.cfg index 9e22a891b3..d1ed458fb7 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,7 +1,7 @@ [metadata] name = biolink_model description = 'A high level datamodel of biological entities and associations' -version = 3.4.0 +version = 3.4.1 url = https://github.com/biolink/biolink-model author = Harold Solbrig diff --git a/setup.py b/setup.py index dab9c24f63..ab4d7f8ce4 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ REQUIREMENTS = FH.readlines() NAME = 'biolink-model' -VERSION = '3.4.0' +VERSION = '3.4.1' DESCRIPTION = 'Biolink Model: A high level datamodel of biological entities and associations' URL = 'https://github.com/biolink/biolink-model' From 4b50a919f67990112f86f00c40ca96d63e1a6727 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 23 May 2023 17:38:09 -0700 Subject: [PATCH 2/6] remove infores import to prevent overwriting with its definitions --- ChangeLog | 4 ++++ biolink-model.yaml | 1 - biolink/model.py | 4 ++-- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/ChangeLog b/ChangeLog index 69202d8e24..ffaa0a8cb7 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,5 +1,9 @@ CHANGES ======= +3.4.1 +----- +recreate wheel with pydantic included + 3.4.0 ----- remove support for dynamic enumerations in anatomical context qualifier diff --git a/biolink-model.yaml b/biolink-model.yaml index 985cf58802..711b0989a6 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -203,7 +203,6 @@ subsets: imports: - linkml:types - - information-resource types: diff --git a/biolink/model.py b/biolink/model.py index 79806af7dc..def5440d4d 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-05-23T23:23:30 +# Generation date: 2023-05-23T17:37:18 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -25,7 +25,7 @@ from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE, XSDDate, XSDTime metamodel_version = "1.7.0" -version = "3.4.0" +version = "3.4.1" # Overwrite dataclasses _init_fn to add **kwargs in __init__ dataclasses._init_fn = dataclasses_init_fn_with_kwargs From 001e06c295feb862d9c2dfd3aeb4c961e872cbb4 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 23 May 2023 17:40:21 -0700 Subject: [PATCH 3/6] gene to phenotypic feature association --- biolink-model.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index 711b0989a6..9dae10c2c3 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -9862,7 +9862,7 @@ classes: - for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype - if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children. - gene to phenotype association: + gene to phenotypic feature association: is_a: gene to disease or phenotypic feature association exact_mappings: - WBVocab:Gene-Phenotype-Association From 89a812e5c43548ff394b47b31551474925732d4e Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 23 May 2023 17:42:16 -0700 Subject: [PATCH 4/6] prep for a release --- biolink-model.yaml | 2 +- setup.cfg | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index 9dae10c2c3..f7c5433ce8 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -6,7 +6,7 @@ license: https://creativecommons.org/publicdomain/zero/1.0/ # Version should be kept in sync with primary Git repository release tag -version: 3.4.1 +version: 3.4.2 ## ------------ diff --git a/setup.cfg b/setup.cfg index d1ed458fb7..12e12ba563 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,7 +1,7 @@ [metadata] name = biolink_model description = 'A high level datamodel of biological entities and associations' -version = 3.4.1 +version = 3.4.2 url = https://github.com/biolink/biolink-model author = Harold Solbrig diff --git a/setup.py b/setup.py index ab4d7f8ce4..4eba042c30 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ REQUIREMENTS = FH.readlines() NAME = 'biolink-model' -VERSION = '3.4.1' +VERSION = '3.4.2' DESCRIPTION = 'Biolink Model: A high level datamodel of biological entities and associations' URL = 'https://github.com/biolink/biolink-model' From ebeeaadd82b8e7c051dee3d573917d821e76654e Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 23 May 2023 17:45:38 -0700 Subject: [PATCH 5/6] add changelog --- ChangeLog | 4 + biolink/pydanticmodel.py | 524 ++++++++++++++++++--------------------- 2 files changed, 248 insertions(+), 280 deletions(-) diff --git a/ChangeLog b/ChangeLog index ffaa0a8cb7..4f6a076f71 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,5 +1,9 @@ CHANGES ======= +3.4.2 +---- +move GeneToPhenotypeAssociation to GeneToPhenotypicFeatureAssociation + 3.4.1 ----- recreate wheel with pydantic included diff --git a/biolink/pydanticmodel.py b/biolink/pydanticmodel.py index 9069614de5..3afbe395ab 100644 --- a/biolink/pydanticmodel.py +++ b/biolink/pydanticmodel.py @@ -12,7 +12,7 @@ metamodel_version = "None" -version = "3.4.0" +version = "3.4.2" class WeakRefShimBaseModel(BaseModel): __slots__ = '__weakref__' @@ -397,19 +397,6 @@ class FDAIDAAdverseEventEnum(str, Enum): -class InformationResourceStatusEnum(str, Enum): - - - released = "released" - - deprecated = "deprecated" - - draft = "draft" - - modified = "modified" - - - class MappingCollection(ConfiguredBaseModel): """ A collection of deprecated mappings. @@ -525,7 +512,7 @@ class Entity(ConfiguredBaseModel): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -545,7 +532,7 @@ class NamedThing(Entity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -568,7 +555,7 @@ class Attribute(NamedThing, OntologyClass): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -591,7 +578,7 @@ class ChemicalRole(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -612,7 +599,7 @@ class BiologicalSex(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -635,7 +622,7 @@ class PhenotypicSex(BiologicalSex): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -658,7 +645,7 @@ class GenotypicSex(BiologicalSex): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -681,7 +668,7 @@ class SeverityValue(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -717,7 +704,7 @@ class OrganismTaxon(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -737,7 +724,7 @@ class Event(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -755,7 +742,7 @@ class AdministrativeEntity(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -777,7 +764,7 @@ class Agent(AdministrativeEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -801,7 +788,7 @@ class InformationContentEntity(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -825,7 +812,7 @@ class StudyResult(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -849,7 +836,7 @@ class StudyVariable(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -873,7 +860,7 @@ class CommonDataElement(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -897,7 +884,7 @@ class ConceptCountAnalysisResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -921,7 +908,7 @@ class ObservedExpectedFrequencyAnalysisResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -945,7 +932,7 @@ class RelativeFrequencyAnalysisResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -969,7 +956,7 @@ class TextMiningResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -993,7 +980,7 @@ class ChiSquaredAnalysisResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1017,7 +1004,7 @@ class LogOddsAnalysisResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1041,7 +1028,7 @@ class Dataset(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1066,7 +1053,7 @@ class DatasetDistribution(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1093,7 +1080,7 @@ class DatasetVersion(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1119,7 +1106,7 @@ class DatasetSummary(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1143,7 +1130,7 @@ class ConfidenceLevel(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1167,7 +1154,7 @@ class EvidenceType(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1196,7 +1183,7 @@ class Publication(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1225,7 +1212,7 @@ class Book(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'book'.""") name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1255,7 +1242,7 @@ class BookChapter(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1287,7 +1274,7 @@ class Serial(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'serial' or 'journal'.""") name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1320,7 +1307,7 @@ class Article(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1353,7 +1340,7 @@ class JournalArticle(Article): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1382,7 +1369,7 @@ class Patent(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1411,7 +1398,7 @@ class WebPage(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1440,7 +1427,7 @@ class PreprintPublication(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1469,7 +1456,7 @@ class DrugLabel(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1496,7 +1483,7 @@ class RetrievalSource(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1532,7 +1519,7 @@ class PhysicalEntity(PhysicalEssence, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1568,7 +1555,7 @@ class Activity(ActivityAndBehavior, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1588,7 +1575,7 @@ class Study(Activity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1608,7 +1595,7 @@ class Procedure(ActivityAndBehavior, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1628,7 +1615,7 @@ class Phenomenon(Occurrent, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1648,7 +1635,7 @@ class Device(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1668,7 +1655,7 @@ class DiagnosticAid(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1696,7 +1683,7 @@ class MaterialSample(SubjectOfInvestigation, PhysicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1716,7 +1703,7 @@ class PlanetaryEntity(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1734,7 +1721,7 @@ class EnvironmentalProcess(PlanetaryEntity, Occurrent): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1752,7 +1739,7 @@ class EnvironmentalFeature(PlanetaryEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1774,7 +1761,7 @@ class GeographicLocation(PlanetaryEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1797,7 +1784,7 @@ class GeographicLocationAtTime(GeographicLocation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1824,7 +1811,7 @@ class BiologicalEntity(ThingWithTaxon, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1860,7 +1847,7 @@ class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1884,7 +1871,7 @@ class MolecularActivity(BiologicalProcessOrActivity, Occurrent, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1908,7 +1895,7 @@ class BiologicalProcess(BiologicalProcessOrActivity, Occurrent, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1930,7 +1917,7 @@ class Pathway(BiologicalProcess, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1952,7 +1939,7 @@ class PhysiologicalProcess(BiologicalProcess, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1974,7 +1961,7 @@ class Behavior(BiologicalProcess, ActivityAndBehavior, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1997,7 +1984,7 @@ class OrganismAttribute(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2020,7 +2007,7 @@ class PhenotypicQuality(OrganismAttribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2041,7 +2028,7 @@ class GeneticInheritance(BiologicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2062,7 +2049,7 @@ class OrganismalEntity(BiologicalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2083,7 +2070,7 @@ class Bacterium(OrganismalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2104,7 +2091,7 @@ class Virus(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2123,7 +2110,7 @@ class CellularOrganism(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2144,7 +2131,7 @@ class Mammal(CellularOrganism, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2165,7 +2152,7 @@ class Human(Mammal, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2184,7 +2171,7 @@ class Plant(CellularOrganism): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2205,7 +2192,7 @@ class Invertebrate(CellularOrganism): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2226,7 +2213,7 @@ class Vertebrate(CellularOrganism): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2247,7 +2234,7 @@ class Fungus(CellularOrganism): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2268,7 +2255,7 @@ class LifeStage(OrganismalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2289,7 +2276,7 @@ class IndividualOrganism(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2310,7 +2297,7 @@ class PopulationOfIndividualOrganisms(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2331,7 +2318,7 @@ class StudyPopulation(PopulationOfIndividualOrganisms): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2352,7 +2339,7 @@ class DiseaseOrPhenotypicFeature(BiologicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2373,7 +2360,7 @@ class Disease(DiseaseOrPhenotypicFeature): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2394,7 +2381,7 @@ class PhenotypicFeature(DiseaseOrPhenotypicFeature): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2415,7 +2402,7 @@ class BehavioralFeature(PhenotypicFeature): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2436,7 +2423,7 @@ class AnatomicalEntity(OrganismalEntity, PhysicalEssence): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2457,7 +2444,7 @@ class CellularComponent(AnatomicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2476,7 +2463,7 @@ class Cell(AnatomicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2495,7 +2482,7 @@ class CellLine(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2514,7 +2501,7 @@ class GrossAnatomicalStructure(AnatomicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2544,7 +2531,7 @@ class RegulatoryRegion(ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, Biologi In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2566,7 +2553,7 @@ class AccessibleDnaRegion(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, G In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2588,7 +2575,7 @@ class TranscriptionFactorBindingSite(RegulatoryRegion, ChemicalEntityOrGeneOrGen In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2621,7 +2608,7 @@ class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneO In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2647,7 +2634,7 @@ class MolecularEntity(ChemicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2673,7 +2660,7 @@ class SmallMolecule(MolecularEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2702,7 +2689,7 @@ class ChemicalMixture(ChemicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2730,7 +2717,7 @@ class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, Physical In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2759,7 +2746,7 @@ class MolecularMixture(ChemicalMixture): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2788,7 +2775,7 @@ class ComplexMolecularMixture(ChemicalMixture): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2817,7 +2804,7 @@ class ProcessedMaterial(ChemicalMixture): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2846,7 +2833,7 @@ class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2869,7 +2856,7 @@ class EnvironmentalFoodContaminant(ChemicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2892,7 +2879,7 @@ class FoodAdditive(ChemicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2921,7 +2908,7 @@ class Food(ChemicalMixture): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2961,7 +2948,7 @@ class Gene(GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3002,7 +2989,7 @@ class MacromolecularComplex(MacromolecularMachineMixin, BiologicalEntity): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3024,7 +3011,7 @@ class NucleosomeModification(GeneProductIsoformMixin, EpigenomicEntity, GenomicE In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") @@ -3047,7 +3034,7 @@ class Genome(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3075,7 +3062,7 @@ class Exon(NucleicAcidEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3103,7 +3090,7 @@ class Transcript(NucleicAcidEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3129,7 +3116,7 @@ class CodingSequence(NucleicAcidEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3150,7 +3137,7 @@ class Polypeptide(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGe In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3172,7 +3159,7 @@ class Protein(Polypeptide, GeneProductMixin): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3194,7 +3181,7 @@ class ProteinIsoform(Protein, GeneProductIsoformMixin): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3215,7 +3202,7 @@ class PosttranslationalModification(GeneProductIsoformMixin, BiologicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") @@ -3237,7 +3224,7 @@ class NucleicAcidSequenceMotif(BiologicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3264,7 +3251,7 @@ class RNAProduct(Transcript, GeneProductMixin): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3293,7 +3280,7 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3320,7 +3307,7 @@ class NoncodingRNAProduct(RNAProduct): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3347,7 +3334,7 @@ class MicroRNA(NoncodingRNAProduct): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3376,7 +3363,7 @@ class SiRNA(NoncodingRNAProduct): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3406,7 +3393,7 @@ class ProteinDomain(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3426,7 +3413,7 @@ class ProteinFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3448,7 +3435,7 @@ class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biologica In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3469,7 +3456,7 @@ class Zygosity(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3492,7 +3479,7 @@ class Genotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3514,7 +3501,7 @@ class Haplotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass) In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3537,7 +3524,7 @@ class SequenceVariant(GenomicEntity, BiologicalEntity, PhysicalEssence, Ontology In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3560,7 +3547,7 @@ class Snv(SequenceVariant): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3582,7 +3569,7 @@ class ReagentTargetedGene(GenomicEntity, BiologicalEntity, PhysicalEssence, Onto In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3605,7 +3592,7 @@ class ClinicalAttribute(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3628,7 +3615,7 @@ class ClinicalMeasurement(ClinicalAttribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3651,7 +3638,7 @@ class ClinicalModifier(ClinicalAttribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3674,7 +3661,7 @@ class ClinicalCourse(ClinicalAttribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3697,7 +3684,7 @@ class Onset(ClinicalCourse): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3717,7 +3704,7 @@ class ClinicalEntity(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3735,7 +3722,7 @@ class ClinicalTrial(ClinicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3753,7 +3740,7 @@ class ClinicalIntervention(ClinicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3774,7 +3761,7 @@ class ClinicalFinding(PhenotypicFeature): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3792,7 +3779,7 @@ class Hospitalization(ClinicalIntervention): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3815,7 +3802,7 @@ class SocioeconomicAttribute(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3836,7 +3823,7 @@ class Case(IndividualOrganism, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3857,7 +3844,7 @@ class Cohort(StudyPopulation, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3893,7 +3880,7 @@ class GenomicBackgroundExposure(ExposureEvent, GeneGroupingMixin, GenomicEntity, This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3925,7 +3912,7 @@ class PathologicalProcess(PathologicalEntityMixin, BiologicalProcess): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3949,7 +3936,7 @@ class PathologicalProcessExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3970,7 +3957,7 @@ class PathologicalAnatomicalStructure(PathologicalEntityMixin, AnatomicalEntity) In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3994,7 +3981,7 @@ class PathologicalAnatomicalExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4018,7 +4005,7 @@ class DiseaseOrPhenotypicFeatureExposure(PathologicalEntityMixin, ExposureEvent, This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4042,7 +4029,7 @@ class ChemicalExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4065,7 +4052,7 @@ class ComplexChemicalExposure(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4089,7 +4076,7 @@ class DrugExposure(ChemicalExposure, ExposureEvent): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4114,7 +4101,7 @@ class DrugToGeneInteractionExposure(DrugExposure, GeneGroupingMixin): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4138,7 +4125,7 @@ class Treatment(ExposureEvent, NamedThing, ChemicalOrDrugOrTreatment): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4162,7 +4149,7 @@ class BioticExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4186,7 +4173,7 @@ class EnvironmentalExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4210,7 +4197,7 @@ class GeographicExposure(EnvironmentalExposure, ExposureEvent): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4234,7 +4221,7 @@ class BehavioralExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4258,7 +4245,7 @@ class SocioeconomicExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: List[str] = Field(..., description="""connects any entity to an attribute""") @@ -4373,7 +4360,7 @@ class Association(Entity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4414,7 +4401,7 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4457,7 +4444,7 @@ class ContributorAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4500,7 +4487,7 @@ class GenotypeToGenotypePartAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4543,7 +4530,7 @@ class GenotypeToGeneAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4586,7 +4573,7 @@ class GenotypeToVariantAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4629,7 +4616,7 @@ class GeneToGeneAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4672,7 +4659,7 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4715,7 +4702,7 @@ class GeneToGeneFamilyAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4773,7 +4760,7 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4816,7 +4803,7 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4860,7 +4847,7 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4943,7 +4930,7 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4987,7 +4974,7 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5031,7 +5018,7 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5082,7 +5069,7 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5125,7 +5112,7 @@ class MolecularActivityToPathwayAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5168,7 +5155,7 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5209,7 +5196,7 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5260,7 +5247,7 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5316,7 +5303,7 @@ class ChemicalAffectsGeneAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5359,7 +5346,7 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5410,7 +5397,7 @@ class MaterialSampleDerivationAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5467,7 +5454,7 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5520,7 +5507,7 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5594,7 +5581,7 @@ class InformationContentEntityToNamedThingAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5653,7 +5640,7 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5696,7 +5683,7 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5745,7 +5732,7 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5788,7 +5775,7 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5832,7 +5819,7 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5876,7 +5863,7 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5919,7 +5906,7 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5969,7 +5956,7 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6020,7 +6007,7 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6071,7 +6058,7 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6122,7 +6109,7 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6173,7 +6160,7 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6229,7 +6216,7 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6279,7 +6266,7 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6291,7 +6278,7 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, -class GeneToPhenotypeAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin): +class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin): sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) @@ -6323,14 +6310,14 @@ class GeneToPhenotypeAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, Ge retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - category: List[Literal["https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation","biolink:GeneToPhenotypeAssociation"]] = Field(["biolink:GeneToPhenotypeAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + category: List[Literal["https://w3id.org/biolink/vocab/GeneToPhenotypicFeatureAssociation","biolink:GeneToPhenotypicFeatureAssociation"]] = Field(["biolink:GeneToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6381,7 +6368,7 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, Gene In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6432,7 +6419,7 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssoc In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6483,7 +6470,7 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityA In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6534,7 +6521,7 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6584,7 +6571,7 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6631,7 +6618,7 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6679,7 +6666,7 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6722,7 +6709,7 @@ class PopulationToPopulationAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6764,7 +6751,7 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6812,7 +6799,7 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -6856,7 +6843,7 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -6911,7 +6898,7 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6959,7 +6946,7 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -7003,7 +6990,7 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -7047,7 +7034,7 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -7091,7 +7078,7 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -7135,7 +7122,7 @@ class OrganismToOrganismAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7176,7 +7163,7 @@ class TaxonToTaxonAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7221,7 +7208,7 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -7273,7 +7260,7 @@ class GeneToExpressionSiteAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7316,7 +7303,7 @@ class SequenceVariantModulatesTreatmentAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7359,7 +7346,7 @@ class FunctionalAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7410,7 +7397,7 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7453,7 +7440,7 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7496,7 +7483,7 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7539,7 +7526,7 @@ class MolecularActivityToChemicalEntityAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7582,7 +7569,7 @@ class MolecularActivityToMolecularActivityAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7623,7 +7610,7 @@ class GeneToGoTermAssociation(FunctionalAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7665,7 +7652,7 @@ class EntityToDiseaseAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7707,7 +7694,7 @@ class EntityToPhenotypicFeatureAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7750,7 +7737,7 @@ class SequenceAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7798,7 +7785,7 @@ class GenomicSequenceLocalization(SequenceAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7841,7 +7828,7 @@ class SequenceFeatureRelationship(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7884,7 +7871,7 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7927,7 +7914,7 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7970,7 +7957,7 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8014,7 +8001,7 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8055,7 +8042,7 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8098,7 +8085,7 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8141,7 +8128,7 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8192,7 +8179,7 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8235,7 +8222,7 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8279,7 +8266,7 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8320,32 +8307,11 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") -class InformationResourceContainer(ConfiguredBaseModel): - """ - A collection of information resources - """ - information_resources: Optional[List[InformationResource]] = Field(default_factory=list, description="""a collection of information resources""") - - - -class InformationResource(ConfiguredBaseModel): - """ - A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb. - """ - status: Optional[InformationResourceStatusEnum] = Field(None, description="""the status of the infores identifier, the default is \"released\"""") - name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - description: Optional[str] = Field(None) - - - # Update forward refs # see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ @@ -8602,7 +8568,7 @@ class InformationResource(ConfiguredBaseModel): GeneToPathwayAssociation.update_forward_refs() VariantToEntityAssociationMixin.update_forward_refs() GeneToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -GeneToPhenotypeAssociation.update_forward_refs() +GeneToPhenotypicFeatureAssociation.update_forward_refs() GeneToDiseaseAssociation.update_forward_refs() CausalGeneToDiseaseAssociation.update_forward_refs() CorrelatedGeneToDiseaseAssociation.update_forward_refs() @@ -8650,6 +8616,4 @@ class InformationResource(ConfiguredBaseModel): OrganismTaxonToOrganismTaxonSpecialization.update_forward_refs() OrganismTaxonToOrganismTaxonInteraction.update_forward_refs() OrganismTaxonToEnvironmentAssociation.update_forward_refs() -InformationResourceContainer.update_forward_refs() -InformationResource.update_forward_refs() From ab2f567c32d37a4c4241e7459b924697c41a7a26 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 23 May 2023 17:47:24 -0700 Subject: [PATCH 6/6] update spelling of specialized --- biolink-model.yaml | 2 +- biolink/model.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index f7c5433ce8..30a066945c 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -609,7 +609,7 @@ slots: in_subset: - translator_minimal narrow_mappings: - # there is an interesting debate here: are these terms "narrower" a.k.a. more specnaialized instances of + # there is an interesting debate here: are these terms "narrower" a.k.a. more specialized instances of # 'biolink:synonym' or should they be binned into their respective namesake class of mappings? # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc. - skos:altLabel diff --git a/biolink/model.py b/biolink/model.py index def5440d4d..a4c4179aea 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -25,7 +25,7 @@ from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE, XSDDate, XSDTime metamodel_version = "1.7.0" -version = "3.4.1" +version = "3.4.2" # Overwrite dataclasses _init_fn to add **kwargs in __init__ dataclasses._init_fn = dataclasses_init_fn_with_kwargs